Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

25766736

DOI Digital object identifier for electronic documents.

10.1093/jac/dkv062

URI

Authors

Vervoort J, Xavier BB, Stewardson A, Coenen S, Godycki-Cwirko M, Adriaenssens N, Kowalczyk A, Lammens C, Harbarth S, Goossens H, Malhotra-Kumar S

Journal

The Journal of antimicrobial chemotherapy

Year

2015

Keywords:

16S rDNA, 16S rRNA, antibiotic resistance, compositional changes, culture independent, faecal flora, gastrointestinal flora, stool, urinary tract infections

OBJECTIVES: The objective was to study changes in the faecal microbiota of patients with uncomplicated urinary tract infections (UTIs) treated with nitrofurantoin and of non-treated healthy controls using 16S rRNA analysis. METHODS: Serial stool samples were collected from patients receiving nitrofurantoin treatment at different timepoints [before treatment (day 1; T1), within 48 h of end of treatment (days 5-15; T2) and 28 days after treatment (days 31-43; T3)], as well as from healthy controls. Direct DNA extraction (PowerSoil DNA Isolation Kit, MoBio Laboratories, Carlsbad, CA, USA) from stool samples was followed by pyrosequencing (454 GS FLX Titanium) of the V3-V5 region of the bacterial 16S rRNA gene. RESULTS: Among UTI patients, mean proportions of the Actinobacteria phylum increased by 19.6% in the first follow-up sample (T2) in comparison with the pretreatment baseline stool sample (T1) (P = 0.026). However, proportions of Actinobacteria reversed to 'normal' pre-antibiotic levels, with a mean difference of 1.0% compared with baseline proportions, in the second follow-up sample (T3). The increase in Actinobacteria was specifically due to an increase in the Bifidobacteriaceae family (Bifidobacterium genus), which constituted 81.0% (95% CI ±7.4%) of this phylum. CONCLUSIONS: No significant impact was observed other than a temporary increase in the beneficial Bifidobacterium genus following nitrofurantoin treatment, which supports its reintroduction into clinical use.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2021/12/11

Curator: Mmarin

Revision editor(s): Mmarin, WikiWorks, Peace Sandy

Subjects

Location of subjects: Belgium; Poland

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Bacterial urinary tract infection

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Control group

Group 1 name Corresponds to the case (exposed) group for case-control studies: Antibiotic treated - T2

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Receiving nitrofurantoin treatment (100 mg three times daily for 3–15 days)

Group 0 sample size Number of subjects in the control (unexposed) group: 5

Group 1 sample size Number of subjects in the case (exposed) group: 8

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: Linear Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Signature 1

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Curated date: 2021/12/11

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Source: Table 1

Description: changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.

Abundance in Group 1: decreased abundance in Antibiotic treated - T2

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Bacteroidota

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Experiment 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2022/01/14

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Antibiotic treated (day 1)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Antibiotic treated (day 5-15)

Group 0 sample size Number of subjects in the control (unexposed) group: 8

Lab analysis

Statistical Analysis

Signature 1

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Curated date: 2022/01/14

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Source: Table 1

Description: changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.

Abundance in Group 1: increased abundance in Antibiotic treated (day 5-15)

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Actinomycetota

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Experiment 3

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2022/01/14

Curator: Mmarin

Revision editor(s): Mmarin, WikiWorks, Peace Sandy

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Control (day 1)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Control (day 5-15)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Did not receive nitrofurantoin treatment

Group 0 sample size Number of subjects in the control (unexposed) group: 5

Group 1 sample size Number of subjects in the case (exposed) group: 5

Lab analysis

Statistical Analysis

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2022/01/14

Curator: Mmarin

Revision editor(s): Mmarin, Peace Sandy, WikiWorks

Source: Table 1

Description: changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.

Abundance in Group 1: increased abundance in Control (day 5-15)

NCBI	Quality Control	Links
Bacteroidota

Revision editor(s): Mmarin, Peace Sandy, WikiWorks